Two recent papers, one in the Journal of Morphology and another in Ornithological Monographs, as well as a ScienceDaily news release titled "Discovery Raises New Doubts About Dinosaur-bird Links," contain criticisms by evolutionists of the dino-to-bird hypothesis that you would normally expect to hear only from skeptics of neo-Darwinism. Their remarks not only cover problems facing the dino-to-birds hypothesis, but also lament the politically motivated drive to push that hypothesis and ignore scientific dissent. The ScienceDaily article observes that some aspects of bird morphology are simply incompatible with the standard hypothesis that birds evolved from maniraptoran theropod dinosaurs:

It's been known for decades that the femur, or thigh bone in birds is largely fixed and makes birds into "knee runners," unlike virtually all other land animals, the [Oregon State University] experts say. What was just discovered, however, is that it's this fixed position of bird bones and musculature that keeps their air-sac lung from collapsing when the bird inhales.

Warm-blooded birds need about 20 times more oxygen than cold-blooded reptiles, and have evolved a unique lung structure that allows for a high rate of gas exchange and high activity level. Their unusual thigh complex is what helps support the lung and prevent its collapse.

"This is fundamental to bird physiology," said Devon Quick, an OSU instructor of zoology who completed this work as part of her doctoral studies. "It's really strange that no one realized this before. The position of the thigh bone and muscles in birds is critical to their lung function, which in turn is what gives them enough lung capacity for flight."

However, every other animal that has walked on land, the scientists said, has a moveable thigh bone that is involved in their motion -- including humans, elephants, dogs, lizards and -- in the ancient past -- dinosaurs.

The implication, the researchers said, is that birds almost certainly did not descend from theropod dinosaurs, such as tyrannosaurus or allosaurus. The findings add to a growing body of evidence in the past two decades that challenge some of the most widely-held beliefs about animal evolution....

"But one of the primary reasons many scientists kept pointing to birds as having descended from dinosaurs was similarities in their lungs," Ruben said. "However, theropod dinosaurs had a moving femur and therefore could not have had a lung that worked like that in birds. Their abdominal air sac, if they had one, would have collapsed. That undercuts a critical piece of supporting evidence for the dinosaur-bird link.

In their technical paper in the Journal of Morphology, Quick and Ruben provide a more detailed explanation of how theropod dinosaurs differ from birds in this important way:

Theropods examined in this study uniformly lacked the specialized sternal and costal features of modern birds (Hillenius and Ruben, 2004a). Theropods also exhibited significantly less pelvic cross-sectional space with which to have accommodated abdominal air-sacs similar in development to those in modern birds. In addition, the deep, vertically-oriented lateral body wall of theropods apparently lacked lateral skeletal support for caudally positioned (e.g., abdominal) air-sacs: the theropod ''lumbar'' rib cage was reduced and the vertical, free-swinging femur almost surely could not have contributed to a rigid lateral abdominal wall (see Fig. 5). Notably, the gastralia (imbricating slender ''belly ribs,'' Fig. 5) do not articulate solidly with other bony elements nor do they significantly invest the lateral body wall (Claessens, 2004b). Thus, in the absence of a bird-like ribcage, a dearth of space to accommodate fully avian sized abdominal air-sacs in the caudal body cavity or a skeletal mechanism to resist their paradoxical collapse, theropods were unlikely to have possessed functional bird-like abdominal air-sacs

Quick and Ruben also provide a potent counterpoint to the argument that theropods were the ancestors of birds because theropods have postcranial pneumatization, i.e. air cavities in their bones:

It has been previously argued that postcranial pneumatization signals the existence of functional abdominal air-sacs in theropods. Supposedly, these air-sacs could have been ventilated via relatively unmodified rib cages with well developed gastralia or uncinate processes or a combination of both (Carrier and Farmer, 2000a; O'Connor and Claessens, 2005; Tickle et al., 2007; Codd et al., 2008). However, there are several reasons to question these arguments. Skeletal pneumatization is well documented in pterosaurs, sauropods, some early birds, numerous theropods and possibly even the Late Triassic archosauriforms Erythrosuchus and Effigia (Nesbitt and Norell, 2006; O'Connor, 2006). Given so wide a phylogenetic distribution, postcranial pneumatization is likely plesiomorphic for Ornithodira (birds, dinosaurs and pterosaurs) and possibly as ancient as basal Archosauria (O'Connor, 2006)....

Interpretation of vertebral pneumatization as a lock-step indicator for the presence of a fully functional avian style lung air-sac system ignores the widespread distribution of posterior, nonvascularized air sacs in many living reptiles and undoubted selective pressures for skeletal mass reduction. Furthermore, as discussed earlier, reconstruction of theropods with modern avian lung air-sac anatomy and function neglects the absence of requisite skeletal morphology necessary for its ventilation in modern forms.

The authors conclude that "there are few data supportive of there having been an avian style lung air-sac system in theropods or that these dinosaurs necessarily possessed cardiovascular structure significantly different from that of crocodilians."

Of course Darwin-skeptics have been noting for years that there are key morphological differences between birds and theropod dinosaurs that challenge claims of an evolutionary link. Another recent extensive review of the standard hypothesis that birds evolved from maniraptoran theropod dinosaurs (called the "BMT" hypothesis) found "no [cladistic analysis-based] statistical difference between the hypothesis that birds were a clade nested within the Maniraptora and the hypothesis that core clades of Maniraptora were actually flying and flightless radiations within the clade bracketed by Archaeopteryx and modern birds (Aves)." (Frances C. James and John A. Pourtless IV, "Cladistics and the Origins of Birds: A Review and Two New Analyses," Ornithological Monographs, 66:1-78 (2009).)

In other words, statistical tests show that when compared to the BMT hypothesis, it's just as likely that the maniraptoran theropod dinosaurs were not the ancestors birds, but were actually descendants of birds and were simply secondarily flightless birds. (Such views are shared by a variety of other experts.) This alternate view is made even more convincing when one considers an admission by zoologist John Ruben in the aforementioned ScienceNews news release. He notes something that many Darwin-skeptics have pointed out in the past, that maniraptoran theropod dinosaurs don't appear in the right place in the fossil record to be ancestors of birds:

"For one thing, birds are found earlier in the fossil record than the dinosaurs they are supposed to have descended from," Ruben said. "That's a pretty serious problem, and there are other inconsistencies with the bird-from-dinosaur theories.

So if it wasn't theropod dinosaurs, then where did birds come from? James and Pourtless's article also reports that under cladistic analyses, a method of comparing morphological traits usually used to enforce the standard "BMT" hypothesis, it's equally possible that birds are descended from a completely different type of non-dinosaurian reptile, perhaps an ancient crocodile-like form, or another primitive group of reptiles, the early archosaurs:

Additional statistical tests showed that both the "early-archosaur" and "crocodylomorph" hypotheses are at least as well supported as the BMT hypothesis. These results show that Theropoda as presently constituted may not be monophyletic and that the verificationist approach of the BMT literature may be producing misleading studies on the origin of birds....

Our cladistic and statistical analyses of our new data set indicate that several predictions derived from the BMT hypothesis are not supported and that alternatives to the BMT are at least equally viable. Altogether, three hypotheses for the origin of birds -- the BMT, early-archosaur, and crocodylomorph hypotheses -- are most compatible with currently available evidence.

(Frances C. James and John A. Pourtless IV, "Cladistics and the Origins of Birds: A Review and Two New Analyses," Ornithological Monographs, 66:1-78 (2009).)

In other words, the cladistic argument that has been used to support the BMT hypothesis has itself been exploded from the inside out. James and Pourtless show that there is much morphological data that contradicts the standard BMT hypothesis, while other alternative hypotheses are at least as compatible with the data.

But these alternative hypotheses are not without their own problems. One problem facing these alternative hypotheses is not that birds arrive before their alleged ancestors (as is the problem with standard BMT hypothesis), but rather that anything remotely qualifying as an possible ancestor of birds appears many tens of millions of years (i.e., 70+ million years) before birds, with no fossils documenting the evolution of the first uncontroverted bird, Archaeopteryx. Needless to say, many evolutionist don't like this hypothesis because it leaves them with an uncomfortably large gap.

The bottom line is that all of the various theories that birds descended from reptiles face some severe difficulties.

"Old Theories Die Hard"
What is most interesting about these papers and the news release is the way they make clear how closed off the mainstream Darwinian scientific community has been to challenges to the dino-bird hypothesis. The ScienceDaily news release states:

"The conclusions add to other evolving evidence that may finally force many paleontologists to reconsider their long-held belief that modern birds are the direct descendants of ancient, meat-eating dinosaurs, OSU researchers say....

OSU research on avian biology and physiology was among the first in the nation to begin calling into question the dinosaur-bird link since the 1990s. Other findings have been made since then, at OSU and other institutions, which also raise doubts. But old theories die hard, Ruben said, especially when it comes to some of the most distinctive and romanticized animal species in world history.

"Frankly, there's a lot of museum politics involved in this, a lot of careers committed to a particular point of view even if new scientific evidence raises questions," Ruben said. In some museum displays, he said, the birds-descended-from-dinosaurs evolutionary theory has been portrayed as a largely accepted fact, with an asterisk pointing out in small type that "some scientists disagree."

Likewise, James and Pourtless's paper in Ornithological Monographs states forthrightly that when it comes to the theropod dinosaur-to-bird hypothesis, "Criticism has usually been dismissed, often with the comment that no more parsimonious alternative has been presented with cladistic methodology," further stating that "uncertainties about the hypothesis that birds are maniraptoran theropods are not receiving enough attention." Their conclusion provides a noteworthy warning about how a lack of scrutiny of the BMT hypothesis has led to unwarranted acceptance of that view:

We have pursued two goals: evaluation of whether the BMT hypothesis is as well supported as has been claimed, and evaluation of alternative hypotheses for the origin of birds within a comparative phylogenetic framework. We conclude that, because of circularity in the construction of matrices, inadequate taxon sampling, insufficiently rigorous application of cladistic methods, and a verificationist approach, the BMT hypothesis has not been subjected to sufficiently rigorous attempts at refutation, and the literature does not provide the claimed overwhelming support. Our analyses and independent data indicate that two of the alternatives to the BMT hypothesis are as probable as the BMT and are potentially supported by specific osteological data. These alternatives are the early-archosaur hypothesis, positing a sister-group relationship between Longisquama and Aves, and a variant of the crocodylomorph hypothesis. Both hypotheses include the proposition that some maniraptorans are actually birds more derived than Archaeopteryx.

(Frances C. James and John A. Pourtless IV, "Cladistics and the Origins of Birds: A Review and Two New Analyses," Ornithological Monographs, 66:1-78 (2009).)

These analyses not only raise significant reasons for doubting the maniraptoran theropod-dinosaur-to-bird ("BMT") hypothesis, but they show that there is much discomfort even within the Darwinian scientific community about how dissent from the BMT hypothesis is not being heard.